HEADER APOPTOSIS 22-APR-08 2ZNE TITLE CRYSTAL STRUCTURE OF ZN2+-BOUND FORM OF DES3-23ALG-2 COMPLEXED WITH TITLE 2 ALIX ABS PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 6; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 2-191; COMPND 5 SYNONYM: APOPTOSIS-LINKED GENE 2 PROTEIN, PROBABLE CALCIUM-BINDING COMPND 6 PROTEIN ALG-2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 16-MERIC PEPTIDE FROM PROGRAMMED CELL DEATH 6-INTERACTING COMPND 10 PROTEIN; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: ALG-2 BINDING SITE, RESIDUES 799-814; COMPND 13 SYNONYM: PDCD6-INTERACTING PROTEIN, ALG-2-INTERACTING PROTEIN 1, COMPND 14 HP95; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDCD6, ALG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3D; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICAL SYNTHESIS; THIS SEQUENCE OCCURS NATURALLY IN SOURCE 14 HUMANS. KEYWDS PENTA-EF-HAND PROTEIN, CALCIUM BINDING PROTEIN, APOPTOSIS, KEYWDS 2 ENDOPLASMIC RETICULUM, MEMBRANE, NUCLEUS, POLYMORPHISM, CYTOPLASM, KEYWDS 3 HOST-VIRUS INTERACTION, PROTEIN TRANSPORT, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.SUZUKI,M.KAWASAKI,T.INUZUKA,T.KAKIUCHI,H.SHIBATA,S.WAKATSUKI,M.MAKI REVDAT 5 01-NOV-23 2ZNE 1 REMARK REVDAT 4 10-NOV-21 2ZNE 1 REMARK SEQADV REVDAT 3 24-FEB-09 2ZNE 1 VERSN REVDAT 2 04-NOV-08 2ZNE 1 JRNL REVDAT 1 09-SEP-08 2ZNE 0 JRNL AUTH H.SUZUKI,M.KAWASAKI,T.INUZUKA,M.OKUMURA,T.KAKIUCHI, JRNL AUTH 2 H.SHIBATA,S.WAKATSUKI,M.MAKI JRNL TITL STRUCTURAL BASIS FOR CA(2+)-DEPENDENT FORMATION OF JRNL TITL 2 ALG-2/ALIX PEPTIDE COMPLEX: CA(2+)/EF3-DRIVEN ARGININE JRNL TITL 3 SWITCH MECHANISM JRNL REF STRUCTURE V. 16 1562 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18940611 JRNL DOI 10.1016/J.STR.2008.07.012 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 21603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1462 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3002 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -0.89000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.233 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.862 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3086 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4179 ; 1.437 ; 1.921 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ;11.891 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;34.055 ;23.693 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 499 ;18.191 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;24.471 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 426 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2446 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1506 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2159 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 152 ; 0.167 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 17 ; 0.095 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 56 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.223 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1798 ; 0.862 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2914 ; 1.635 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1354 ; 2.122 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1265 ; 3.510 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000028187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23278 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1HQV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% 2-PROPANOL, 0.1M CACODYLATE, 0.2M REMARK 280 ZINC ACETATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.77800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 105.77800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.72450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.25450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.72450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.25450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 105.77800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.72450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.25450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 105.77800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.72450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.25450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -170.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -342.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 2 REMARK 465 ALA B 2 REMARK 465 ASP B 24 REMARK 465 GLN C 1 REMARK 465 GLY D 13 REMARK 465 TYR D 14 REMARK 465 SER D 15 REMARK 465 GLN D 16 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 56 -168.10 -121.11 REMARK 500 ARG A 143 7.20 -153.14 REMARK 500 GLN A 172 63.24 38.04 REMARK 500 ILE A 190 -67.96 -97.59 REMARK 500 ARG B 39 19.83 53.74 REMARK 500 ASN B 61 113.96 -31.37 REMARK 500 GLU B 75 15.19 -156.98 REMARK 500 TYR C 8 159.10 163.08 REMARK 500 SER C 15 57.27 -102.05 REMARK 500 PRO D 4 34.77 -84.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR C 8 PRO C 9 -132.20 REMARK 500 PRO D 9 GLY D 10 -69.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 991 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 992 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 993 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 994 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 991 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 992 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 993 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 994 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 995 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZN8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZN2+-BOUND FORM OF ALG-2 REMARK 900 RELATED ID: 2ZN9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CA2+-BOUND FORM OF DES3-20ALG-2 REMARK 900 RELATED ID: 2ZND RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CA2+-FREE FORM OF DES3-20ALG-2 DBREF 2ZNE A 2 191 UNP O75340 PDCD6_HUMAN 2 191 DBREF 2ZNE B 2 191 UNP O75340 PDCD6_HUMAN 2 191 DBREF 2ZNE C 1 16 UNP Q8WUM4 PDC6I_HUMAN 799 814 DBREF 2ZNE D 1 16 UNP Q8WUM4 PDC6I_HUMAN 799 814 SEQADV 2ZNE A UNP O75340 ALA 3 DELETION SEQADV 2ZNE A UNP O75340 TYR 4 DELETION SEQADV 2ZNE A UNP O75340 SER 5 DELETION SEQADV 2ZNE A UNP O75340 TYR 6 DELETION SEQADV 2ZNE A UNP O75340 ARG 7 DELETION SEQADV 2ZNE A UNP O75340 PRO 8 DELETION SEQADV 2ZNE A UNP O75340 GLY 9 DELETION SEQADV 2ZNE A UNP O75340 PRO 10 DELETION SEQADV 2ZNE A UNP O75340 GLY 11 DELETION SEQADV 2ZNE A UNP O75340 ALA 12 DELETION SEQADV 2ZNE A UNP O75340 GLY 13 DELETION SEQADV 2ZNE A UNP O75340 PRO 14 DELETION SEQADV 2ZNE A UNP O75340 GLY 15 DELETION SEQADV 2ZNE A UNP O75340 PRO 16 DELETION SEQADV 2ZNE A UNP O75340 ALA 17 DELETION SEQADV 2ZNE A UNP O75340 ALA 18 DELETION SEQADV 2ZNE A UNP O75340 GLY 19 DELETION SEQADV 2ZNE A UNP O75340 ALA 20 DELETION SEQADV 2ZNE A UNP O75340 ALA 21 DELETION SEQADV 2ZNE A UNP O75340 LEU 22 DELETION SEQADV 2ZNE A UNP O75340 PRO 23 DELETION SEQADV 2ZNE A UNP O75340 ALA 3 DELETION SEQADV 2ZNE A UNP O75340 TYR 4 DELETION SEQADV 2ZNE A UNP O75340 SER 5 DELETION SEQADV 2ZNE A UNP O75340 TYR 6 DELETION SEQADV 2ZNE B UNP O75340 ARG 7 DELETION SEQADV 2ZNE B UNP O75340 PRO 8 DELETION SEQADV 2ZNE B UNP O75340 GLY 9 DELETION SEQADV 2ZNE B UNP O75340 PRO 10 DELETION SEQADV 2ZNE B UNP O75340 GLY 11 DELETION SEQADV 2ZNE B UNP O75340 ALA 12 DELETION SEQADV 2ZNE B UNP O75340 GLY 13 DELETION SEQADV 2ZNE B UNP O75340 PRO 14 DELETION SEQADV 2ZNE B UNP O75340 GLY 15 DELETION SEQADV 2ZNE B UNP O75340 PRO 16 DELETION SEQADV 2ZNE B UNP O75340 ALA 17 DELETION SEQADV 2ZNE B UNP O75340 ALA 18 DELETION SEQADV 2ZNE B UNP O75340 GLY 19 DELETION SEQADV 2ZNE B UNP O75340 ALA 20 DELETION SEQADV 2ZNE B UNP O75340 ALA 21 DELETION SEQADV 2ZNE B UNP O75340 LEU 22 DELETION SEQADV 2ZNE B UNP O75340 PRO 23 DELETION SEQADV 2ZNE SER C 15 UNP Q8WUM4 CYS 813 ENGINEERED MUTATION SEQADV 2ZNE SER D 15 UNP Q8WUM4 CYS 813 ENGINEERED MUTATION SEQRES 1 A 169 ALA ASP GLN SER PHE LEU TRP ASN VAL PHE GLN ARG VAL SEQRES 2 A 169 ASP LYS ASP ARG SER GLY VAL ILE SER ASP THR GLU LEU SEQRES 3 A 169 GLN GLN ALA LEU SER ASN GLY THR TRP THR PRO PHE ASN SEQRES 4 A 169 PRO VAL THR VAL ARG SER ILE ILE SER MET PHE ASP ARG SEQRES 5 A 169 GLU ASN LYS ALA GLY VAL ASN PHE SER GLU PHE THR GLY SEQRES 6 A 169 VAL TRP LYS TYR ILE THR ASP TRP GLN ASN VAL PHE ARG SEQRES 7 A 169 THR TYR ASP ARG ASP ASN SER GLY MET ILE ASP LYS ASN SEQRES 8 A 169 GLU LEU LYS GLN ALA LEU SER GLY PHE GLY TYR ARG LEU SEQRES 9 A 169 SER ASP GLN PHE HIS ASP ILE LEU ILE ARG LYS PHE ASP SEQRES 10 A 169 ARG GLN GLY ARG GLY GLN ILE ALA PHE ASP ASP PHE ILE SEQRES 11 A 169 GLN GLY CYS ILE VAL LEU GLN ARG LEU THR ASP ILE PHE SEQRES 12 A 169 ARG ARG TYR ASP THR ASP GLN ASP GLY TRP ILE GLN VAL SEQRES 13 A 169 SER TYR GLU GLN TYR LEU SER MET VAL PHE SER ILE VAL SEQRES 1 B 169 ALA ASP GLN SER PHE LEU TRP ASN VAL PHE GLN ARG VAL SEQRES 2 B 169 ASP LYS ASP ARG SER GLY VAL ILE SER ASP THR GLU LEU SEQRES 3 B 169 GLN GLN ALA LEU SER ASN GLY THR TRP THR PRO PHE ASN SEQRES 4 B 169 PRO VAL THR VAL ARG SER ILE ILE SER MET PHE ASP ARG SEQRES 5 B 169 GLU ASN LYS ALA GLY VAL ASN PHE SER GLU PHE THR GLY SEQRES 6 B 169 VAL TRP LYS TYR ILE THR ASP TRP GLN ASN VAL PHE ARG SEQRES 7 B 169 THR TYR ASP ARG ASP ASN SER GLY MET ILE ASP LYS ASN SEQRES 8 B 169 GLU LEU LYS GLN ALA LEU SER GLY PHE GLY TYR ARG LEU SEQRES 9 B 169 SER ASP GLN PHE HIS ASP ILE LEU ILE ARG LYS PHE ASP SEQRES 10 B 169 ARG GLN GLY ARG GLY GLN ILE ALA PHE ASP ASP PHE ILE SEQRES 11 B 169 GLN GLY CYS ILE VAL LEU GLN ARG LEU THR ASP ILE PHE SEQRES 12 B 169 ARG ARG TYR ASP THR ASP GLN ASP GLY TRP ILE GLN VAL SEQRES 13 B 169 SER TYR GLU GLN TYR LEU SER MET VAL PHE SER ILE VAL SEQRES 1 C 16 GLN GLY PRO PRO TYR PRO THR TYR PRO GLY TYR PRO GLY SEQRES 2 C 16 TYR SER GLN SEQRES 1 D 16 GLN GLY PRO PRO TYR PRO THR TYR PRO GLY TYR PRO GLY SEQRES 2 D 16 TYR SER GLN HET ZN A 991 1 HET ZN A 992 1 HET ZN A 993 1 HET ZN A 994 1 HET NA A 995 1 HET ZN B 991 1 HET ZN B 992 1 HET ZN B 993 1 HET ZN B 994 1 HET NA B 1 1 HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 5 ZN 8(ZN 2+) FORMUL 9 NA 2(NA 1+) FORMUL 15 HOH *68(H2 O) HELIX 1 1 ASP A 24 ASP A 36 1 13 HELIX 2 2 SER A 44 LEU A 52 1 9 HELIX 3 3 ASN A 61 ASP A 73 1 13 HELIX 4 4 ASN A 81 ASP A 103 1 23 HELIX 5 5 LYS A 112 GLY A 123 1 12 HELIX 6 6 SER A 127 ASP A 139 1 13 HELIX 7 7 ALA A 147 ARG A 167 1 21 HELIX 8 8 TYR A 180 SER A 189 1 10 HELIX 9 9 SER B 26 ASP B 36 1 11 HELIX 10 10 ASP B 45 ALA B 51 1 7 HELIX 11 11 ASN B 61 ASP B 73 1 13 HELIX 12 12 ASN B 81 ASP B 103 1 23 HELIX 13 13 ASP B 111 PHE B 122 1 12 HELIX 14 14 SER B 127 ASP B 139 1 13 HELIX 15 15 ALA B 147 ASP B 169 1 23 HELIX 16 16 TYR B 180 VAL B 191 1 12 SHEET 1 A 2 ILE A 110 ASP A 111 0 SHEET 2 A 2 GLN A 145 ILE A 146 -1 O ILE A 146 N ILE A 110 SHEET 1 B 2 TRP A 175 SER A 179 0 SHEET 2 B 2 TRP B 175 SER B 179 -1 O VAL B 178 N ILE A 176 SHEET 1 C 2 ILE B 43 SER B 44 0 SHEET 2 C 2 GLY B 79 VAL B 80 -1 O VAL B 80 N ILE B 43 CISPEP 1 PRO C 12 GLY C 13 0 -28.94 CISPEP 2 GLN D 1 GLY D 2 0 -7.90 SITE 1 AC1 5 ASP A 36 ASP A 38 SER A 40 VAL A 42 SITE 2 AC1 5 GLU A 47 SITE 1 AC2 6 ASP A 103 ASP A 105 SER A 107 MET A 109 SITE 2 AC2 6 GLU A 114 ZN A 994 SITE 1 AC3 5 ASP A 171 ASP A 173 NA A 995 HOH A1000 SITE 2 AC3 5 HOH A1018 SITE 1 AC4 5 ASP A 105 ASP A 111 GLU A 114 ZN A 992 SITE 2 AC4 5 HOH A1021 SITE 1 AC5 6 ASP B 36 ASP B 38 SER B 40 VAL B 42 SITE 2 AC5 6 GLU B 47 HOH B1028 SITE 1 AC6 6 ASP B 103 ASP B 105 SER B 107 MET B 109 SITE 2 AC6 6 GLU B 114 ZN B 994 SITE 1 AC7 5 NA B 1 ASP B 171 ASP B 173 HOH B1007 SITE 2 AC7 5 HOH B1017 SITE 1 AC8 5 ASP B 105 ASP B 111 GLN B 145 ZN B 992 SITE 2 AC8 5 HOH B 995 SITE 1 AC9 7 ASP B 169 ASP B 171 ASP B 173 TRP B 175 SITE 2 AC9 7 ZN B 993 HOH B1005 HOH B1017 SITE 1 BC1 6 ASP A 169 ASP A 171 ASP A 173 TRP A 175 SITE 2 BC1 6 ZN A 993 HOH A1019 CRYST1 47.449 88.509 211.556 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021075 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004727 0.00000